QMIR 2026
Week 2: Reproducible Research with R, Quarto & Git
Tristan Muno What is Reproducible Research?
- For small or one-off tasks, this workflow may seem excessive
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- Its advantages become substantial as projects increase in scope, duration, or collaboration
The Workflow
Output embedded in documents
## Example of embedded figure
```r
#| echo: true
#| eval: true
#| label: fig-demo
#| fig-cap: "A demo figure"
library(forcats)
library(ggplot2)
demo_data <- data.frame(
country = c("Germany", "France", "Italy", "Spain", "Poland"),
pop = c(83, 67, 60, 47, 38)
)
ggplot(
data = demo_data,
aes(x = fct_reorder(country, pop), y = pop)
) +
geom_col(fill = "white", color = "black") +
theme_bw() +
labs(x = "Country", y = "Population in Million")
```
@fig-demo shows an embedded figure.Example of embedded figure
View source
library(forcats)
library(ggplot2)
demo_data <- data.frame(
country = c("Germany", "France", "Italy", "Spain", "Poland"),
pop = c(83, 67, 60, 47, 38)
)
ggplot(
data = demo_data,
aes(x = fct_reorder(country, pop), y = pop)
) +
geom_col(fill = "white", color = "black") +
theme_bw() +
labs(x = "Country", y = "Population in Million")
Figure 3 shows an embedded figure.
Version Control with Git
- Repository (repo) \(\rightarrow\) project folder with memory 🗂️
- git init \(\rightarrow\) Turns a normal folder into a Git repository 🚀
- Stage (git add) \(\rightarrow\) Select changes you want to include in the next snapshot 📦
- Commit \(\rightarrow\) A saved snapshot of staged changes 📸
- Commit message \(\rightarrow\) Short explanation of what and why you changed something 💬
- History (git log) \(\rightarrow\) Timeline of all committed snapshots 🕰️
- Remote \(\rightarrow\) Online copy of your repository (e.g., GitHub) ☁️
Version Control with Git
